ngs MiSeq pipeline vs GATK best practices
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12 days ago
tinakopale • 0

Hi,

I am working with WES data and I am trying to build a pipeline with the help of GATK best practices. I would like to know the difference between pipeline that is built-in in Illumina sequencer and GATk Best Practices pipeline.

Is the VQSR used in built in software of Illumina? Why should I follow Best practices when everything is built in sequencer, can you please help me to see the difference?

Thank you very much

pipeline gatk MiSeq ngs • 125 views
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If the pipeline built-in in Illumina sequencers you are refering to is the DRAGEN pipeline, then there aren't many differences, and the plan is for them to be the same:

DRAGEN-GATK Update: Let's get more specific

The hardware-accelerated DRAGEN pipeline found in Illumina sequencers is subscription-based, but a lot faster, so it may suit the needs of big sequencing centers and service providers.

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Thank you, it is not the Dragan pipeline that is built-in.

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